Get 1GB RAM like Cas says.
The rest you can’t go wrong with as nearly everything you mentioned is included with the OS… (E.g. Tomcat is part of the developer tools install, java and JWS are all pre-installed. The UI relies heavily on OpenGL…)
Not sure why you mentioned that “in theory” you wanted at least OS X. You can’t buy a Mac with anything else, and if you did you would be quite an idiot (no offense ).
Java 5.0 (formerly 1.5) will only be available for the next version of OS X if history is to repeat itself. And OS X 10.4 (also named “Tiger”) isn’t to be released for almost a year. Previews of Tiger and Tiger (Java) on Tiger (OS) are available now. But I think it will be a while before it is usable.
Updates for the JRE/JDK are available less frequently for the Mac… but Apple has caught up now to Sun’s Java releases for the most part so it’s not bad.
I run Eclipse on my Mac, with only 512MB RAM… and it I can get by. The Eclipse team has really improved the Mac support with the 3.0 release.
LWJGL still isn’t working properly on Mac… but if you are the one to make it work, Cas will buy you a brand new to of the line Mac… so that’s a bonus. I 've been hoping to help out in that department myself… but dammit if my day job doesn’t require too much time.
JOGL works well and is supported by an Apple engineer. Xith3D works.
Quicken is available - though it costs more for the Mac version because Intuit are money sucking weasel scum.
You will have to go with a newer version of Word (which has sucked for many years andding useless features that are always in the way and buggering the UI so now everything that you want to do is hard or non-intuitive to do. It is easier to use TeX at this point.)
Office 2004 for the Mac has some features that debut in the Mac version… it seems Microsoft’s Mac Business Unit is doing a decent job.
The built-in browser “Safari” is excellent.
I dont’ know of compatible software for the familiy tree stuff… but it sounds like a nice Java project
If you intened to get a Laptop (you didn’t say if you were replacing or complementing your current machine - sounds like you are replacing) it might be a good idea to wait a bit and see if any G5-based laptops happen soon… but they have been rumoured for some time. Though the current G4 crop are super machines. I have a previous generation G4 laptop and I love it.
You can use a combo-drive (CD-RW/DVD) or a “superdrive” (DVD-R/CD-RW), the “iLife” package that is included with the machine is excellent.
Mac comes with a C/C++/Objective-C/Java IDE called Xcode. It is decent, but there is a learning curve, as the UI is unlike most other IDEs. The Objective-C GUI builder “Interface Builder” is excellent, but they dont’ have great support for Java in Xcode yet… though it improves with each version. For Java work stick with Eclipse in any case.
You will likely hate hte one-button mouse/trackpad. Plug in a 3-button USB wheel-mouse and it will work as you expect it to though.
Browse the Apple.com pages to get a feel for what is included with the Apple hardware and OS… you will find there is a lot there that comes bundled with the machine/OS.